Log file opened on Fri Dec 12 16:22:52 2014 Host: etna.ii.uib.no pid: 14003 nodeid: 0 nnodes: 1 Gromacs version: VERSION 4.6.6 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled GPU support: disabled invsqrt routine: gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library: fftpack (built-in) Large file support: enabled RDTSCP usage: enabled Built on: Wed Aug 13 11:30:34 CEST 2014 Built by: venken@etna.ii.uib.no [CMAKE] Build OS/arch: Linux 2.6.32-431.11.2.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand: Intel(R) Xeon(R) CPU E5-2609 v2 @ 2.50GHz Build CPU family: 6 Model: 62 Stepping: 4 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU cc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) C compiler flags: -mavx -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG :-) G R O M A C S (-: Gyas ROwers Mature At Cryogenic Speed :-) VERSION 4.6.6 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) mdrun (-: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 -------- -------- --- Thank You --- -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 -------- -------- --- Thank You --- -------- -------- Input Parameters: integrator = md nsteps = 50000 init-step = 0 cutoff-scheme = Group ns_type = Grid nstlist = 5 ndelta = 2 nstcomm = 100 comm-mode = Linear nstlog = 5000 nstxout = 500000 nstvout = 500000 nstfout = 500000 nstcalcenergy = 100 nstenergy = 5000 nstxtcout = 500 init-t = 0 delta-t = 0.002 xtcprec = 1000 fourierspacing = 0.12 nkx = 64 nky = 64 nkz = 96 pme-order = 4 ewald-rtol = 1e-05 ewald-geometry = 0 epsilon-surface = 0 optimize-fft = FALSE ePBC = xyz bPeriodicMols = FALSE bContinuation = FALSE bShakeSOR = FALSE etc = V-rescale bPrintNHChains = FALSE nsttcouple = 5 epc = Berendsen epctype = Semiisotropic nstpcouple = 5 tau-p = 1 ref-p (3x3): ref-p[ 0]={ 1.01300e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 1.01300e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.01300e+00} compress (3x3): compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 verlet-buffer-drift = 0.005 rlist = 1.2 rlistlong = 1.4 nstcalclr = 5 rtpi = 0.05 coulombtype = PME coulomb-modifier = None rcoulomb-switch = 0 rcoulomb = 1.2 vdwtype = Switch vdw-modifier = None rvdw-switch = 1.2 rvdw = 1.4 epsilon-r = 1 epsilon-rf = inf tabext = 1 implicit-solvent = No gb-algorithm = Still gb-epsilon-solvent = 80 nstgbradii = 1 rgbradii = 1 gb-saltconc = 0 gb-obc-alpha = 1 gb-obc-beta = 0.8 gb-obc-gamma = 4.85 gb-dielectric-offset = 0.009 sa-algorithm = Ace-approximation sa-surface-tension = 2.05016 DispCorr = No bSimTemp = FALSE free-energy = no nwall = 0 wall-type = 9-3 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = no rotation = FALSE disre = No disre-weighting = Conservative disre-mixed = FALSE dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orires-fc = 0 orires-tau = 0 nstorireout = 100 dihre-fc = 0 em-stepsize = 0.01 em-tol = 10 niter = 20 fc-stepsize = 0 nstcgsteep = 1000 nbfgscorr = 10 ConstAlg = Lincs shake-tol = 0.0001 lincs-order = 4 lincs-warnangle = 30 lincs-iter = 1 bd-fric = 0 ld-seed = 1993 cos-accel = 0 deform (3x3): deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} adress = FALSE userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 628.983 41424.9 67870.1 ref-t: 310 310 310 tau-t: 0.1 0.1 0.1 anneal: No No No ann-npoints: 0 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 0 energygrp-flags[ 1]: 0 0 efield-x: n = 0 efield-xt: n = 0 efield-y: n = 0 efield-yt: n = 0 efield-z: n = 0 efield-zt: n = 0 bQMMM = FALSE QMconstraints = 0 QMMMscheme = 0 scalefactor = 1 qm-opts: ngQM = 0 Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 0.413 nm, LJ-14, atoms 9191 9208 multi-body bonded interactions: 0.413 nm, Proper Dih., atoms 9191 9208 Minimum cell size due to bonded interactions: 0.455 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm Estimated maximum distance required for P-LINCS: 0.819 nm This distance will limit the DD cell size, you can override this with -rcon Using 0 separate PME nodes, as there are too few total nodes for efficient splitting Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 1.024 nm The maximum allowed number of cells is: X 7 Y 7 Z 10 Domain decomposition grid 4 x 1 x 2, separate PME nodes 0 PME domain decomposition: 8 x 1 x 1 Domain decomposition nodeid 0, coordinates 0 0 0 Using 8 MPI threads Detecting CPU-specific acceleration. Present hardware specification: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2609 v2 @ 2.50GHz Family: 6 Model: 62 Stepping: 4 Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Acceleration most likely to fit this hardware: AVX_256 Acceleration selected at GROMACS compile time: AVX_256 Table routines are used for coulomb: FALSE Table routines are used for vdw: TRUE Will do PME sum in reciprocal space. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- --- Thank You --- -------- -------- Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Using shifted Lennard-Jones, switch between 1.2 and 1.4 nm Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.4 System total charge: 0.000 Generated table with 1200 data points for Ewald. Tabscale = 500 points/nm Generated table with 1200 data points for LJ6Switch. Tabscale = 500 points/nm Generated table with 1200 data points for LJ12Switch. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1200 data points for 1-4 LJ12. Tabscale = 500 points/nm Potential shift: LJ r^-12: 0.000 r^-6 0.000, Ewald 0.000e+00 Initialized non-bonded Ewald correction tables, spacing: 7.23e-04 size: 3322 Removing pbc first time Pinning threads with an auto-selected logical core stride of 1 Initializing Parallel LINear Constraint Solver ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess P-LINCS: A Parallel Linear Constraint Solver for molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 116-122 -------- -------- --- Thank You --- -------- -------- The number of constraints is 20801 There are inter charge-group constraints, will communicate selected coordinates each lincs iteration ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- --- Thank You --- -------- -------- Linking all bonded interactions to atoms There are 116439 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: X 1 Z 1 The initial domain decomposition cell size is: X 1.81 nm Z 5.14 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.400 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.400 nm multi-body bonded interactions (-rdd) 1.400 nm atoms separated by up to 5 constraints (-rcon) 1.813 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Z 1 The minimum size for domain decomposition cells is 1.400 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.77 Z 0.27 The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.400 nm two-body bonded interactions (-rdd) 1.400 nm multi-body bonded interactions (-rdd) 1.400 nm atoms separated by up to 5 constraints (-rcon) 1.400 nm Making 2D domain decomposition grid 4 x 1 x 2, home cell index 0 0 0 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 -------- -------- --- Thank You --- -------- -------- There are: 54888 Atoms Charge group distribution at step 0: 3975 4047 3976 4148 3953 4055 4047 4063 Grid: 6 x 13 x 12 cells Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 8.82e-06 Initial temperature: 309.363 K Started mdrun on node 0 Thu Jan 1 01:00:00 1970 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 3.58088e+04 3.96844e+04 1.25507e+02 -4.29327e+01 5.35450e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.65477e+04 1.07068e+04 -5.72553e+02 -5.72870e+05 -7.29847e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -5.65652e+05 1.41496e+05 -4.24156e+05 3.09630e+02 -6.69474e+03 Constr. rmsd 1.35930e-05 DD step 4 load imb.: force 3.5% DD step 4999 load imb.: force 1.2% Step Time Lambda 5000 10.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.19368e+04 3.96543e+04 4.29612e+02 -4.71015e+01 6.44253e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.53856e+04 1.04323e+04 -5.79100e+02 -4.91376e+05 -7.33972e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -4.65832e+05 1.41257e+05 -3.24575e+05 3.09108e+02 -2.03458e+02 Constr. rmsd 8.34805e-06 DD step 9999 load imb.: force 2.6% Step Time Lambda 10000 20.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.08753e+04 3.88377e+04 4.98851e+02 -3.58555e+01 6.11979e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.51487e+04 9.63515e+03 -5.85414e+02 -4.91964e+05 -7.35609e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -4.69123e+05 1.42422e+05 -3.26701e+05 3.11657e+02 -8.77252e+01 Constr. rmsd 8.38708e-06 Writing checkpoint, step 13860 at Fri Dec 12 16:37:53 2014 DD step 14999 load imb.: force 2.3% Step Time Lambda 15000 30.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.10114e+04 3.86607e+04 4.60092e+02 -3.37232e+01 6.20615e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.47173e+04 8.79557e+03 -5.87540e+02 -4.90198e+05 -7.52234e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -4.67925e+05 1.41334e+05 -3.26590e+05 3.09277e+02 1.06932e+01 Constr. rmsd 7.93203e-06 DD step 19999 load imb.: force 2.0% Step Time Lambda 20000 40.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.05468e+04 3.81601e+04 4.10902e+02 -1.63617e+01 6.11352e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.40083e+04 9.24794e+03 -5.87342e+02 -4.92526e+05 -7.71894e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -4.70378e+05 1.41196e+05 -3.29182e+05 3.08974e+02 -1.90386e+02 Constr. rmsd 8.33861e-06 DD step 24999 load imb.: force 2.8% Step Time Lambda 25000 50.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.06543e+04 3.79692e+04 3.94162e+02 -4.27802e+01 6.14632e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.40684e+04 1.05198e+04 -5.86832e+02 -4.93177e+05 -7.65434e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -4.69845e+05 1.41164e+05 -3.28682e+05 3.08904e+02 1.97480e+02 Constr. rmsd 7.96827e-06 Writing checkpoint, step 27620 at Fri Dec 12 16:52:53 2014 DD step 29999 load imb.: force 2.7% Step Time Lambda 30000 60.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.08123e+04 3.79431e+04 4.34050e+02 -3.61279e+01 6.14604e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.41079e+04 9.57494e+03 -5.87458e+02 -4.93341e+05 -7.73631e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -4.70898e+05 1.41816e+05 -3.29082e+05 3.10332e+02 -1.57406e+01 Constr. rmsd 8.49614e-06 DD step 34999 load imb.: force 3.2% Step Time Lambda 35000 70.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.05337e+04 3.78708e+04 4.09303e+02 -3.30396e+01 6.18333e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.36174e+04 8.72958e+03 -5.87898e+02 -4.93231e+05 -7.87078e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -4.71613e+05 1.41728e+05 -3.29885e+05 3.10139e+02 -8.51544e+01 Constr. rmsd 8.11448e-06 DD step 39999 load imb.: force 2.1% Step Time Lambda 40000 80.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.04089e+04 3.74118e+04 3.94949e+02 -5.35612e+01 6.21188e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.33997e+04 9.74822e+03 -5.88524e+02 -4.93626e+05 -7.85047e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -4.71343e+05 1.40499e+05 -3.30844e+05 3.07449e+02 4.25394e+01 Constr. rmsd 7.98951e-06 Writing checkpoint, step 41260 at Fri Dec 12 17:07:53 2014 DD step 44999 load imb.: force 4.6% Step Time Lambda 45000 90.00000 0.00000 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.06589e+04 3.78428e+04 3.73144e+02 -3.03530e+01 6.17739e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.37052e+04 9.80956e+03 -5.89792e+02 -4.94162e+05 -7.75016e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -4.71375e+05 1.41379e+05 -3.29996e+05 3.09376e+02 -3.74047e+00 Constr. rmsd 7.90629e-06 DD step 49999 load imb.: force 3.2% Step Time Lambda 50000 100.00000 0.00000 Writing checkpoint, step 50000 at Fri Dec 12 17:17:33 2014 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.06832e+04 3.69731e+04 4.30535e+02 -2.71200e+01 6.06052e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.33390e+04 1.09698e+04 -5.89094e+02 -4.96305e+05 -7.93412e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -4.73078e+05 1.41683e+05 -3.31395e+05 3.10041e+02 -8.58593e+01 Constr. rmsd 8.63312e-06 <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> Statistics over 50001 steps using 501 frames Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.10967e+04 3.83324e+04 4.21556e+02 -3.42886e+01 6.26205e+03 Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. -7.43681e+04 9.88255e+03 -5.86280e+02 -4.92888e+05 -7.59080e+03 Potential Kinetic En. Total Energy Temperature Pressure (bar) -4.69473e+05 1.41565e+05 -3.27908e+05 3.09782e+02 -1.86612e+01 Constr. rmsd 0.00000e+00 Box-X Box-Y Box-Z 7.21073e+00 7.21073e+00 1.02575e+01 Total Virial (kJ/mol) 4.73830e+04 -3.35641e+02 -1.72294e+02 -3.37159e+02 4.71240e+04 1.04122e+02 -1.77564e+02 1.01377e+02 4.79675e+04 Pressure (bar) -2.89694e+01 2.01443e+01 8.04584e+00 2.02397e+01 -1.78781e+01 -4.57953e+00 8.37475e+00 -4.40933e+00 -9.13621e+00 Epot (kJ/mol) Coul-SR LJ-SR LJ-LR Coul-14 LJ-14 Other-Other 2.02835e+04 -3.22742e+04 -2.34361e+02 -8.01603e+04 5.81109e+03 Other-rest -5.21853e+04 -6.16708e+03 -1.14525e+02 0.00000e+00 0.00000e+00 rest-rest -4.60987e+05 4.83238e+04 -2.37394e+02 5.79223e+03 4.50958e+02 T-Protein T-POPC T-SOL 3.09972e+02 3.09930e+02 3.09689e+02 M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernels NxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) V&F=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops ----------------------------------------------------------------------------- NB VdW [V&F] 359315.578132 359315.578 0.3 NB VdW [F] 5840169.647860 5840169.648 5.4 NB VdW & Elec. [V&F] 1235790.412930 1235790.413 1.1 NB VdW & Elec. [F] 85166680.917735 85166680.918 78.9 1,4 nonbonded interactions 2781.905637 250371.507 0.2 Calc Weights 8233.364664 296401.128 0.3 Spread Q Bspline 175645.112832 351290.226 0.3 Gather F Bspline 175645.112832 1053870.677 1.0 3D-FFT 730805.015808 5846440.126 5.4 Solve PME 204.804096 13107.462 0.0 NS-Pairs 290261.490732 6095491.305 5.6 Reset In Box 322.672264 968.017 0.0 CG-CoM 548.989776 1646.969 0.0 Propers 3412.518249 781466.679 0.7 Impropers 17.350347 3608.872 0.0 Virial 552.535248 9945.634 0.0 Stop-CM 27.553776 275.538 0.0 P-Coupling 2744.454888 16466.729 0.0 Calc-Ekin 1097.869776 29642.484 0.0 Lincs 1778.506198 106710.372 0.1 Lincs-Mat 40758.398112 163033.592 0.2 Constraint-V 4660.966026 37287.728 0.0 Constraint-Vir 1271.643458 30519.443 0.0 Settle 678.765248 219241.175 0.2 (null) 0.850017 0.000 0.0 ----------------------------------------------------------------------------- Total 107909742.222 100.0 ----------------------------------------------------------------------------- D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 66254.6 av. #atoms communicated per step for LINCS: 2 x 9255.7 Average load imbalance: 2.5 % Part of the total run time spent waiting due to load imbalance: 1.1 % R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles % ----------------------------------------------------------------------------- Domain decomp. 8 1 10001 55.716 1111.624 1.7 DD comm. load 8 1 501 0.008 0.157 0.0 Neighbor search 8 1 10001 770.328 15369.364 23.5 Comm. coord. 8 1 50001 6.303 125.752 0.2 Force 8 1 50001 2045.223 40805.678 62.3 Wait + Comm. F 8 1 50001 7.069 141.036 0.2 PME mesh 8 1 50001 317.002 6324.722 9.7 Write traj. 8 1 104 0.214 4.274 0.0 Update 8 1 50001 20.033 399.692 0.6 Constraints 8 1 50001 54.006 1077.517 1.6 Comm. energies 8 1 10001 0.401 7.994 0.0 Rest 8 5.188 103.511 0.2 ----------------------------------------------------------------------------- Total 8 3281.490 65471.321 100.0 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- PME redist. X/F 8 1 100002 130.148 2596.682 4.0 PME spread/gather 8 1 100002 75.627 1508.896 2.3 PME 3D-FFT 8 1 100002 90.992 1815.447 2.8 PME 3D-FFT Comm. 8 1 100002 9.994 199.388 0.3 PME solve 8 1 50001 10.086 201.225 0.3 ----------------------------------------------------------------------------- Core t (s) Wall t (s) (%) Time: 26176.700 3281.490 797.7 54:41 (ns/day) (hour/ns) Performance: 2.633 9.115 Finished mdrun on node 0 Fri Dec 12 17:17:34 2014